Starting phenix.real_space_refine on Tue Dec 31 09:28:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2s_15105/12_2024/8a2s_15105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2s_15105/12_2024/8a2s_15105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2s_15105/12_2024/8a2s_15105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2s_15105/12_2024/8a2s_15105.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2s_15105/12_2024/8a2s_15105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2s_15105/12_2024/8a2s_15105.cif" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9170 2.51 5 N 2450 2.21 5 O 3401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15141 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 145 Classifications: {'water': 145} Link IDs: {None: 144} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "E" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.92, per 1000 atoms: 0.52 Number of scatterers: 15141 At special positions: 0 Unit cell: (94.52, 87.57, 193.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 15 15.00 Mg 5 11.99 O 3401 8.00 N 2450 7.00 C 9170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 53.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.103A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.690A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.532A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.556A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 368 removed outlier: 4.235A pdb=" N SER C 368 " --> pdb=" O ALA C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.103A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.690A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.533A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.557A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 368 removed outlier: 4.235A pdb=" N SER A 368 " --> pdb=" O ALA A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.102A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.690A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.533A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.557A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 368 removed outlier: 4.236A pdb=" N SER B 368 " --> pdb=" O ALA B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.103A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.690A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.533A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.557A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 368 removed outlier: 4.235A pdb=" N SER D 368 " --> pdb=" O ALA D 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.103A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.690A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.533A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.557A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 368 removed outlier: 4.235A pdb=" N SER E 368 " --> pdb=" O ALA E 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 368' Processing helix chain 'E' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.829A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.829A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.353A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.866A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.351A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.903A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.600A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.352A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.600A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.352A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 743 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.88 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4520 1.33 - 1.45: 2105 1.45 - 1.57: 8045 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14860 Sorted by residual: bond pdb=" O4 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O4 PO4 D 403 " pdb=" P PO4 D 403 " ideal model delta sigma weight residual 1.568 1.492 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.492 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 14855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 19570 1.60 - 3.19: 452 3.19 - 4.79: 113 4.79 - 6.38: 20 6.38 - 7.98: 15 Bond angle restraints: 20170 Sorted by residual: angle pdb=" PA ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sigma weight residual 120.50 128.48 -7.98 3.00e+00 1.11e-01 7.07e+00 angle pdb=" PA ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sigma weight residual 120.50 128.46 -7.96 3.00e+00 1.11e-01 7.04e+00 angle pdb=" PA ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sigma weight residual 120.50 128.43 -7.93 3.00e+00 1.11e-01 6.98e+00 angle pdb=" PA ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sigma weight residual 120.50 128.42 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" PA ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sigma weight residual 120.50 128.42 -7.92 3.00e+00 1.11e-01 6.96e+00 ... (remaining 20165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 8780 35.96 - 71.92: 130 71.92 - 107.88: 10 107.88 - 143.85: 5 143.85 - 179.81: 5 Dihedral angle restraints: 8930 sinusoidal: 3615 harmonic: 5315 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.19 179.81 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.21 179.79 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.21 179.79 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1187 0.040 - 0.080: 750 0.080 - 0.120: 269 0.120 - 0.161: 29 0.161 - 0.201: 5 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 2237 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " 0.021 2.00e-02 2.50e+03 1.04e-02 2.70e+00 pdb=" CG TRP B 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " 0.021 2.00e-02 2.50e+03 1.04e-02 2.68e+00 pdb=" CG TRP D 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 340 " 0.021 2.00e-02 2.50e+03 1.03e-02 2.68e+00 pdb=" CG TRP C 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP C 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP C 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 340 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 340 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 340 " 0.004 2.00e-02 2.50e+03 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 92 2.39 - 3.01: 8360 3.01 - 3.64: 24359 3.64 - 4.27: 41727 4.27 - 4.90: 64186 Nonbonded interactions: 138724 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 506 " model vdw 1.758 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 515 " model vdw 1.780 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 559 " model vdw 1.800 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 527 " model vdw 1.851 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 526 " model vdw 1.860 2.170 ... (remaining 138719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.530 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 14860 Z= 0.572 Angle : 0.677 7.978 20170 Z= 0.338 Chirality : 0.053 0.201 2240 Planarity : 0.005 0.044 2570 Dihedral : 14.102 179.806 5520 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.64 % Allowed : 3.22 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1800 helix: -2.19 (0.14), residues: 775 sheet: -0.30 (0.25), residues: 330 loop : 1.26 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 340 HIS 0.005 0.002 HIS B 173 PHE 0.016 0.002 PHE B 262 TYR 0.008 0.002 TYR A 143 ARG 0.006 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 262 time to evaluate : 1.760 Fit side-chains REVERT: C 28 ARG cc_start: 0.8243 (ttm170) cc_final: 0.8026 (ttm170) REVERT: C 121 GLN cc_start: 0.8463 (tt0) cc_final: 0.8258 (tt0) REVERT: A 44 MET cc_start: 0.8413 (mmm) cc_final: 0.8201 (mmt) REVERT: A 191 LYS cc_start: 0.8441 (tttm) cc_final: 0.8200 (ttmm) REVERT: B 41 GLN cc_start: 0.7252 (tt0) cc_final: 0.6595 (tp-100) REVERT: B 64 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8587 (pp) REVERT: B 121 GLN cc_start: 0.8331 (tt0) cc_final: 0.8075 (tt0) REVERT: B 125 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 211 ASP cc_start: 0.7917 (t70) cc_final: 0.7637 (t70) REVERT: B 355 MET cc_start: 0.8207 (mmm) cc_final: 0.7962 (mmm) REVERT: D 41 GLN cc_start: 0.6948 (tt0) cc_final: 0.6351 (tp-100) REVERT: D 57 GLU cc_start: 0.7397 (tt0) cc_final: 0.7118 (mt-10) REVERT: D 128 ASN cc_start: 0.7942 (m110) cc_final: 0.7678 (t0) REVERT: E 50 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7528 (mtpt) REVERT: E 214 GLU cc_start: 0.8210 (mt-10) cc_final: 0.8000 (mt-10) outliers start: 10 outliers final: 5 residues processed: 272 average time/residue: 1.6417 time to fit residues: 484.7784 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 225 ASN A 314 GLN B 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14860 Z= 0.173 Angle : 0.595 7.558 20170 Z= 0.290 Chirality : 0.046 0.196 2240 Planarity : 0.004 0.029 2570 Dihedral : 11.974 179.683 2068 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.54 % Allowed : 8.87 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1800 helix: -0.12 (0.19), residues: 740 sheet: -0.10 (0.25), residues: 330 loop : 1.90 (0.26), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE D 262 TYR 0.010 0.001 TYR B 143 ARG 0.005 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 1.866 Fit side-chains REVERT: C 28 ARG cc_start: 0.8245 (ttm170) cc_final: 0.8037 (ttm170) REVERT: C 225 ASN cc_start: 0.7782 (m-40) cc_final: 0.7570 (m110) REVERT: A 44 MET cc_start: 0.8382 (mmm) cc_final: 0.8180 (mtt) REVERT: A 64 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9113 (pp) REVERT: A 66 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8507 (m) REVERT: A 191 LYS cc_start: 0.8399 (tttm) cc_final: 0.8143 (ttmm) REVERT: B 41 GLN cc_start: 0.7263 (tt0) cc_final: 0.6614 (tp-100) REVERT: B 95 ARG cc_start: 0.7653 (mtt-85) cc_final: 0.7416 (mtp85) REVERT: B 121 GLN cc_start: 0.8254 (tt0) cc_final: 0.8034 (tt0) REVERT: B 211 ASP cc_start: 0.7856 (t70) cc_final: 0.7628 (t70) REVERT: B 355 MET cc_start: 0.8194 (mmm) cc_final: 0.7972 (mmm) REVERT: D 41 GLN cc_start: 0.6924 (tt0) cc_final: 0.6325 (tp40) REVERT: D 128 ASN cc_start: 0.7927 (m110) cc_final: 0.7703 (t0) REVERT: E 50 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7517 (mtpt) REVERT: E 66 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8207 (m) REVERT: E 214 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7893 (mt-10) outliers start: 24 outliers final: 9 residues processed: 227 average time/residue: 1.6659 time to fit residues: 409.4964 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 176 optimal weight: 0.0070 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 59 GLN A 225 ASN B 246 GLN E 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14860 Z= 0.212 Angle : 0.597 7.251 20170 Z= 0.291 Chirality : 0.046 0.186 2240 Planarity : 0.004 0.029 2570 Dihedral : 11.357 178.257 2060 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.06 % Allowed : 10.03 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1800 helix: 0.48 (0.19), residues: 750 sheet: 0.11 (0.26), residues: 330 loop : 1.88 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE D 262 TYR 0.008 0.001 TYR A 143 ARG 0.007 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 1.717 Fit side-chains REVERT: C 123 MET cc_start: 0.8622 (mmt) cc_final: 0.8415 (mmt) REVERT: C 225 ASN cc_start: 0.7752 (m-40) cc_final: 0.7519 (m110) REVERT: A 64 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9110 (pp) REVERT: A 66 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8521 (m) REVERT: A 191 LYS cc_start: 0.8409 (tttm) cc_final: 0.8154 (ttmm) REVERT: B 41 GLN cc_start: 0.7254 (tt0) cc_final: 0.6590 (tp-100) REVERT: B 95 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7389 (mtp85) REVERT: B 211 ASP cc_start: 0.7857 (t70) cc_final: 0.7651 (t70) REVERT: B 355 MET cc_start: 0.8217 (mmm) cc_final: 0.7999 (mmm) REVERT: D 41 GLN cc_start: 0.6934 (tt0) cc_final: 0.6321 (tp40) REVERT: D 64 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8542 (pp) REVERT: D 125 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: D 128 ASN cc_start: 0.7939 (m110) cc_final: 0.7728 (t0) REVERT: D 355 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7239 (mtp) REVERT: E 50 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7517 (mtpt) REVERT: E 117 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7462 (mt-10) REVERT: E 214 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7894 (mt-10) REVERT: E 355 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7584 (mtp) outliers start: 32 outliers final: 14 residues processed: 220 average time/residue: 1.6050 time to fit residues: 382.5618 Evaluate side-chains 203 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN A 225 ASN A 353 GLN B 246 GLN D 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14860 Z= 0.172 Angle : 0.573 6.858 20170 Z= 0.276 Chirality : 0.045 0.180 2240 Planarity : 0.004 0.039 2570 Dihedral : 10.996 179.627 2060 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.80 % Allowed : 11.70 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1800 helix: 0.72 (0.20), residues: 750 sheet: 0.14 (0.26), residues: 335 loop : 1.98 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE D 262 TYR 0.008 0.001 TYR A 143 ARG 0.007 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 2.174 Fit side-chains REVERT: C 123 MET cc_start: 0.8613 (mmt) cc_final: 0.8355 (mmt) REVERT: C 225 ASN cc_start: 0.7766 (m-40) cc_final: 0.7550 (m110) REVERT: A 64 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9121 (pp) REVERT: A 66 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8520 (m) REVERT: A 191 LYS cc_start: 0.8406 (tttm) cc_final: 0.8143 (ttmm) REVERT: A 355 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7846 (mmm) REVERT: B 41 GLN cc_start: 0.7257 (tt0) cc_final: 0.6593 (tp-100) REVERT: B 95 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7386 (mtp85) REVERT: B 355 MET cc_start: 0.8206 (mmm) cc_final: 0.7984 (mmm) REVERT: D 41 GLN cc_start: 0.6936 (tt0) cc_final: 0.6330 (tp40) REVERT: D 64 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8602 (pp) REVERT: D 125 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: D 128 ASN cc_start: 0.7918 (m110) cc_final: 0.7709 (t0) REVERT: D 355 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7255 (mtp) REVERT: E 50 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7513 (mtpt) REVERT: E 117 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7477 (mt-10) REVERT: E 214 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7868 (mt-10) REVERT: E 234 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7761 (t) REVERT: E 355 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7610 (mtp) outliers start: 28 outliers final: 13 residues processed: 200 average time/residue: 1.6827 time to fit residues: 364.6512 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 156 optimal weight: 0.0050 chunk 43 optimal weight: 0.2980 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN A 225 ASN B 225 ASN B 246 GLN E 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14860 Z= 0.294 Angle : 0.635 7.131 20170 Z= 0.313 Chirality : 0.049 0.198 2240 Planarity : 0.004 0.032 2570 Dihedral : 11.172 172.260 2060 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.86 % Allowed : 11.70 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1800 helix: 0.60 (0.19), residues: 765 sheet: 0.18 (0.26), residues: 335 loop : 1.79 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 340 HIS 0.006 0.002 HIS E 87 PHE 0.014 0.002 PHE D 262 TYR 0.008 0.001 TYR A 143 ARG 0.006 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.907 Fit side-chains REVERT: C 125 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: C 225 ASN cc_start: 0.7797 (m-40) cc_final: 0.7568 (m110) REVERT: A 64 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9119 (pp) REVERT: A 66 THR cc_start: 0.8766 (t) cc_final: 0.8560 (m) REVERT: A 191 LYS cc_start: 0.8428 (tttm) cc_final: 0.8182 (ttmm) REVERT: B 41 GLN cc_start: 0.7283 (tt0) cc_final: 0.6625 (tp-100) REVERT: B 64 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8516 (pp) REVERT: B 355 MET cc_start: 0.8238 (mmm) cc_final: 0.7990 (mmm) REVERT: D 41 GLN cc_start: 0.6939 (tt0) cc_final: 0.6311 (tp40) REVERT: D 64 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8554 (pp) REVERT: D 125 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: D 128 ASN cc_start: 0.7919 (m110) cc_final: 0.7654 (t0) REVERT: D 355 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7240 (mtp) REVERT: E 50 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7477 (mtpt) REVERT: E 214 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7893 (mt-10) REVERT: E 215 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8073 (mppt) REVERT: E 234 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7806 (t) REVERT: E 355 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7626 (mtp) outliers start: 29 outliers final: 14 residues processed: 207 average time/residue: 1.6623 time to fit residues: 372.6863 Evaluate side-chains 208 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14860 Z= 0.300 Angle : 0.637 7.138 20170 Z= 0.315 Chirality : 0.049 0.197 2240 Planarity : 0.004 0.042 2570 Dihedral : 11.187 173.054 2060 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.06 % Allowed : 11.90 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1800 helix: 0.61 (0.19), residues: 765 sheet: 0.17 (0.26), residues: 335 loop : 1.76 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 340 HIS 0.005 0.001 HIS C 173 PHE 0.015 0.002 PHE D 262 TYR 0.007 0.001 TYR D 166 ARG 0.008 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.807 Fit side-chains REVERT: C 125 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: C 225 ASN cc_start: 0.7802 (m-40) cc_final: 0.7589 (m110) REVERT: A 64 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9107 (pp) REVERT: A 191 LYS cc_start: 0.8429 (tttm) cc_final: 0.8182 (ttmm) REVERT: B 41 GLN cc_start: 0.7286 (tt0) cc_final: 0.6626 (tp-100) REVERT: B 64 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8515 (pp) REVERT: B 95 ARG cc_start: 0.7645 (mtt-85) cc_final: 0.7402 (mtp85) REVERT: B 355 MET cc_start: 0.8260 (mmm) cc_final: 0.8005 (mmm) REVERT: D 41 GLN cc_start: 0.6934 (tt0) cc_final: 0.6304 (tp40) REVERT: D 64 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8560 (pp) REVERT: D 128 ASN cc_start: 0.7919 (m110) cc_final: 0.7641 (t0) REVERT: D 355 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7235 (mtp) REVERT: E 25 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7260 (p0) REVERT: E 50 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7476 (mtpt) REVERT: E 64 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8375 (pp) REVERT: E 117 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7497 (mt-10) REVERT: E 214 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7897 (mt-10) REVERT: E 215 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8072 (mppt) REVERT: E 234 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7851 (t) REVERT: E 355 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7642 (mtp) outliers start: 32 outliers final: 16 residues processed: 208 average time/residue: 1.7404 time to fit residues: 392.4587 Evaluate side-chains 209 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14860 Z= 0.248 Angle : 0.613 6.991 20170 Z= 0.301 Chirality : 0.048 0.192 2240 Planarity : 0.004 0.043 2570 Dihedral : 11.007 172.088 2060 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.99 % Allowed : 12.09 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1800 helix: 0.68 (0.19), residues: 765 sheet: 0.21 (0.26), residues: 335 loop : 1.78 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 340 HIS 0.004 0.001 HIS C 173 PHE 0.013 0.001 PHE D 262 TYR 0.007 0.001 TYR A 143 ARG 0.009 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.975 Fit side-chains REVERT: C 125 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: C 225 ASN cc_start: 0.7817 (m-40) cc_final: 0.7585 (m110) REVERT: A 64 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9106 (pp) REVERT: A 191 LYS cc_start: 0.8421 (tttm) cc_final: 0.8166 (ttmm) REVERT: A 355 MET cc_start: 0.8276 (mmm) cc_final: 0.7900 (mmm) REVERT: B 41 GLN cc_start: 0.7294 (tt0) cc_final: 0.6628 (tp-100) REVERT: B 64 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 95 ARG cc_start: 0.7664 (mtt-85) cc_final: 0.7413 (mtp85) REVERT: B 355 MET cc_start: 0.8232 (mmm) cc_final: 0.7970 (mmm) REVERT: D 41 GLN cc_start: 0.6934 (tt0) cc_final: 0.6308 (tp40) REVERT: D 64 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8602 (pp) REVERT: D 128 ASN cc_start: 0.7911 (m110) cc_final: 0.7639 (t0) REVERT: D 355 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7236 (mtp) REVERT: E 25 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7239 (p0) REVERT: E 50 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7481 (mtpt) REVERT: E 95 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.7130 (mtt180) REVERT: E 214 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7885 (mt-10) REVERT: E 215 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8049 (mppt) REVERT: E 234 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7850 (t) REVERT: E 355 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7626 (mtp) outliers start: 31 outliers final: 17 residues processed: 204 average time/residue: 1.6868 time to fit residues: 372.9184 Evaluate side-chains 204 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 136 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14860 Z= 0.157 Angle : 0.569 6.584 20170 Z= 0.275 Chirality : 0.045 0.176 2240 Planarity : 0.004 0.039 2570 Dihedral : 10.566 178.874 2060 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.74 % Allowed : 12.35 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1800 helix: 0.89 (0.20), residues: 750 sheet: 0.27 (0.26), residues: 335 loop : 1.98 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.003 0.001 HIS A 161 PHE 0.009 0.001 PHE E 31 TYR 0.008 0.001 TYR C 143 ARG 0.009 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 1.962 Fit side-chains REVERT: C 125 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: C 225 ASN cc_start: 0.7798 (m-40) cc_final: 0.7590 (m110) REVERT: A 64 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9110 (pp) REVERT: A 191 LYS cc_start: 0.8393 (tttm) cc_final: 0.8133 (ttmm) REVERT: A 355 MET cc_start: 0.8249 (mmm) cc_final: 0.7891 (mmm) REVERT: B 41 GLN cc_start: 0.7290 (tt0) cc_final: 0.6631 (tp-100) REVERT: B 64 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8502 (pp) REVERT: B 95 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7330 (mtp85) REVERT: B 355 MET cc_start: 0.8198 (mmm) cc_final: 0.7962 (mmm) REVERT: D 41 GLN cc_start: 0.6938 (tt0) cc_final: 0.6310 (tp40) REVERT: D 64 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8584 (pp) REVERT: D 125 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: D 128 ASN cc_start: 0.7896 (m110) cc_final: 0.7640 (t0) REVERT: D 355 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7228 (mtp) REVERT: E 25 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7197 (p0) REVERT: E 50 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7462 (mtpt) REVERT: E 95 ARG cc_start: 0.7468 (mtt-85) cc_final: 0.7149 (mtt180) REVERT: E 215 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7994 (mppt) REVERT: E 234 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7897 (t) REVERT: E 355 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7603 (mtp) outliers start: 27 outliers final: 13 residues processed: 197 average time/residue: 1.7012 time to fit residues: 362.6966 Evaluate side-chains 202 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 0.4980 chunk 151 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN B 246 GLN E 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14860 Z= 0.172 Angle : 0.575 6.617 20170 Z= 0.278 Chirality : 0.045 0.173 2240 Planarity : 0.004 0.038 2570 Dihedral : 10.345 178.698 2060 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.61 % Allowed : 12.54 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.20), residues: 1800 helix: 0.92 (0.20), residues: 750 sheet: 0.32 (0.26), residues: 335 loop : 2.00 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.007 0.001 HIS E 87 PHE 0.009 0.001 PHE D 262 TYR 0.008 0.001 TYR C 143 ARG 0.008 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.713 Fit side-chains REVERT: C 125 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: C 225 ASN cc_start: 0.7786 (m-40) cc_final: 0.7573 (m110) REVERT: A 64 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9135 (pp) REVERT: A 191 LYS cc_start: 0.8393 (tttm) cc_final: 0.8133 (ttmm) REVERT: A 355 MET cc_start: 0.8250 (mmm) cc_final: 0.7882 (mmm) REVERT: B 41 GLN cc_start: 0.7277 (tt0) cc_final: 0.6626 (tp-100) REVERT: B 95 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7328 (mtp85) REVERT: B 355 MET cc_start: 0.8199 (mmm) cc_final: 0.7980 (mmm) REVERT: D 41 GLN cc_start: 0.6939 (tt0) cc_final: 0.6313 (tp40) REVERT: D 64 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8582 (pp) REVERT: D 125 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: D 128 ASN cc_start: 0.7883 (m110) cc_final: 0.7634 (t0) REVERT: D 355 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7240 (mtp) REVERT: E 25 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7188 (p0) REVERT: E 50 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7465 (mtpt) REVERT: E 95 ARG cc_start: 0.7472 (mtt-85) cc_final: 0.7145 (mtt90) REVERT: E 215 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8004 (mppt) REVERT: E 234 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7920 (t) REVERT: E 355 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7589 (mtp) outliers start: 25 outliers final: 12 residues processed: 197 average time/residue: 1.7579 time to fit residues: 374.1985 Evaluate side-chains 198 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN B 40 HIS B 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14860 Z= 0.178 Angle : 0.578 6.522 20170 Z= 0.280 Chirality : 0.046 0.169 2240 Planarity : 0.004 0.037 2570 Dihedral : 10.219 175.884 2060 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.41 % Allowed : 12.80 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.20), residues: 1800 helix: 0.92 (0.20), residues: 750 sheet: 0.34 (0.26), residues: 335 loop : 1.99 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE D 262 TYR 0.007 0.001 TYR C 143 ARG 0.008 0.000 ARG E 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 1.738 Fit side-chains REVERT: C 125 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: A 64 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9142 (pp) REVERT: A 191 LYS cc_start: 0.8393 (tttm) cc_final: 0.8134 (ttmm) REVERT: A 355 MET cc_start: 0.8251 (mmm) cc_final: 0.7887 (mmm) REVERT: B 41 GLN cc_start: 0.7276 (tt0) cc_final: 0.6628 (tp-100) REVERT: B 355 MET cc_start: 0.8201 (mmm) cc_final: 0.7989 (mmm) REVERT: D 41 GLN cc_start: 0.6939 (tt0) cc_final: 0.6317 (tp40) REVERT: D 64 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8589 (pp) REVERT: D 128 ASN cc_start: 0.7885 (m110) cc_final: 0.7627 (t0) REVERT: D 355 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7245 (mtp) REVERT: E 50 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7467 (mtpt) REVERT: E 95 ARG cc_start: 0.7469 (mtt-85) cc_final: 0.7149 (mtt90) REVERT: E 215 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8000 (mppt) REVERT: E 234 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7918 (t) REVERT: E 355 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7604 (mtp) outliers start: 22 outliers final: 14 residues processed: 190 average time/residue: 1.7012 time to fit residues: 350.6355 Evaluate side-chains 201 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN A 246 GLN A 353 GLN B 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.098981 restraints weight = 15068.684| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.15 r_work: 0.3018 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14860 Z= 0.396 Angle : 0.689 7.303 20170 Z= 0.344 Chirality : 0.052 0.210 2240 Planarity : 0.005 0.042 2570 Dihedral : 11.034 172.325 2060 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.22 % Allowed : 12.93 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1800 helix: 0.59 (0.19), residues: 765 sheet: 0.23 (0.26), residues: 335 loop : 1.79 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP D 340 HIS 0.006 0.002 HIS C 173 PHE 0.018 0.002 PHE D 262 TYR 0.010 0.002 TYR D 166 ARG 0.008 0.001 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6334.43 seconds wall clock time: 114 minutes 34.10 seconds (6874.10 seconds total)